I'm new on this forum and I want first of all to thanks Mario for this amazing framework.
I'm currently create a simple puzzle game as my first Android game and I'm using libgdx.
My game use 3d rendering done with Blender and YafaRay and because they can be big (about 800KB in png) I think JPEG format fit better for this kind of image.
I was using TexturePacker on my desktop start method to automatically group them into atlas images and everything works fine except for the file format.
Actually TexturePacker does support only png format as output and because it was very easy I did few changes to make it support PNG and JPEG based on a parameter you pass (by default is PNG).
If you want to use just add the following line to your Settings object:
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settings.defaultFileFormat = FileFormat.JPEG;
I attached the patch and the file.